Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 1 1 1 1 0.958333333333333
biological_process el 1 1 1 1 0.958333333333333
biological_process ka 1 1 1 1 0.958333333333333
biological_process rf 1 1 1 1 0.958333333333333
disease ct 1 1 1 1 0.958333333333333
disease el 1 1 1 1 0.958333333333333
disease ka 1 1 1 1 0.958333333333333
disease node2vec 1 1 1 1 0.958333333333333
disease rf 1 1 1 1 0.958333333333333
genetic_interaction_weighted ct 0.819444444444444 1 0.5 1 0.966442953020134
genetic_interaction_weighted el 1 1 0.666666666666667 1 0.96
genetic_interaction_weighted ka 1 1 1 1 0.96
genetic_interaction_weighted rf 0.819444444444444 1 0.5 1 0.966442953020134
molecular_function ct 1 1 1 1 0.923076923076923
molecular_function el 1 1 0 1 0.923076923076923
molecular_function ka 1 1 0 1 0.923076923076923
molecular_function node2vec 1 1 0 0 1
molecular_function rf 1 1 0 1 0.923076923076923
pathway ct 0.551724137931034 1 0.333333333333333 1 0.918032786885246
pathway el 0.448275862068966 1 0.166666666666667 1 0.935483870967742
pathway ka 1 1 1 1 0.90625
pathway node2vec 1 1 0.5 1 0.90625
pathway rf 0.481896551724139 1 0.166666666666667 1 0.935483870967742
phenotype ct 1 1 0 1 0.956521739130435
phenotype el 1 1 0 1 0.956521739130435
phenotype ka 1 1 1 1 0.956521739130435
phenotype node2vec 1 1 0.5 1 0.956521739130435
phenotype rf 1 1 0.487500000000011 1 0.956521739130435
protein_interaction ct 0.902777777777778 1 0.166666666666667 1 0.972602739726027
protein_interaction el 0.847222222222222 1 0.166666666666667 1 0.972602739726027
protein_interaction ka 1 1 0.833333333333333 1 0.96
protein_interaction node2vec 0.860763888888889 1 0.333333333333333 1 0.972972972972973
protein_interaction rf 0.888888888888889 1 0.166666666666667 1 0.972602739726027

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 1 1 0.666666666666667 1 0.96
integration_mean_by_presence el 1 1 0.5 1 0.96
integration_mean_by_presence ka 0.638888888888889 0.986111111111111 0 1 0.965034965034965
integration_mean_by_presence node2vec 1 1 1 1 0.96
integration_mean_by_presence rf 0.611111111111111 1 0.5 1 0.966442953020134
mean ct 1 1 0.666666666666667 1 0.96
mean el 1 1 1 1 0.96
mean ka 0.333333333333333 1 0 1 0.972222222222222
mean node2vec 1 1 1 1 0.96
mean rf 1 1 1 1 0.96

Backup Pairs Coverage By Layer

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels